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I am a student and wanted to get into road biking for less, but may be in over my head already. I got ahold of an old Cannondale R1000 CAD2 frame w/ carbon fork, wheels, sprockets, and fancy shift handle brake combos all in good condition for cheap, but I am sans derailleurs and brakes. Besides the rear derailleur hanger that I am told will be near impossible to find so i might just make, which more modern components will fit, and what determines whether they will fit? The rear wheel has a 9-sp cassette and there are three sprockets in front. How about the ultegra series (though there seem to be many different models)?

So you need:[*]rear derailler hanger[*]rear derailler[*]front derailler
The rear derailler hanger should't be that difficult to find, if it's within the past 10 years, and since it comes with a triple crank and 9-speed sprockets, I'm assuming that the bike is from within the last 10 years. You may have to contact Cannondale to find one, or just go to a bike shop that's a Cannondale dealer and they should be able to get one.

Getting the right deraillers will depend on whether you have Shimano components. If your brake-shift levers have a cable popping out of the inner side and then curving in towards the frame, you have Shimano. If your brake shifters have both the brake cables and derailler cables routed under the handlebar tape, then you have Campagnolo components.

Assuming that you have Shimano components, you need a long-cage rear derailler and a triple-compatible front derailler. A triple crank means a wider ranger of gears, which means a wider range of chain slack that the rear derailler will need to take up, so you need a long-cage rear derailler. A triple-compatible front derailler will have a longer cage as well, to be able to handle the wider range of gearing.
If you want to go cheap, you should go with Shimano 105 or Tiagra components. They will work flawlessly, but be a touch heavier or not as nicely polished as Ultegra.
Remember: triple-compatible rear and front derailler. Good luck.

Also, with your front derailler, make sure you get the right mount. Some front deraillers are "braze-on" meaning that there's a little tab on the right side of the seat tube, that the front derailler bolts on to. If there's no such thing on your bike, then you need a typical clamp-on front derailler that clamps around the seat tube. You need to know the diameter of the seat tube (probably 31.8mm for your bike) to purchase one.

Cannondale has used the same hanger since 1991 and is readily avaible from any LBS, not just a Cannondale shop. A 105 deraillier isn't too terribly expensive and are quite capable. You can get by with inexpensive Tekro brakes for now.